Genome-wide identification, bioinformatics and expression analysis of HD-Zip gene family in peach

Wang, Zhe; Wu, Xuelian; Zhang, Binbin; Xiao, Yuansong; Guo, Jian Chun; Liu, Jin; Chen, Qiuju; Peng, Futian

doi:10.1186/s12870-023-04061-w

Cited by 12 publications

(7 citation statements)

References 51 publications

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“…Notably, longer introns were found in HD-ZIP III and IV compared to the other two subfamilies. This pattern is consistent with findings in many other species, such as sesame (Wei et al, 2019), Prunus mume (Li et al, 2019), and peach (Wang et al, 2023). Longer introns are favored in the course of gene evolution, as it promotes the efficiency of natural selection by enhancing recombination between two adjacent exons (Jo and Choi, 2015).…”

Section: The Evolutionary Dynamics Of Hd-zip Gene Familysupporting

confidence: 90%

Genome-wide characterization and expression profiling of the HD-ZIP gene family in Acoraceae under salinity and cold stress

Zhang,

Zhao,

Huang

et al. 2024

Front. Plant Sci.

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The Homeodomain-Leucine Zipper (HD-ZIP) transcription factors play a pivotal role in governing various aspects of plant growth, development, and responses to abiotic stress. Despite the well-established importance of HD-ZIPs in many plants, their functions in Acoraceae, the basal lineage of monocots, remain largely unexplored. Using recently published whole-genome data, we identified 137 putative HD-ZIPs in two Acoraceae species, Acorus gramineus and Acorus calamus. These HD-ZIP genes were further classified into four subfamilies (I, II, III, IV) based on phylogenetic and conserved motif analyses, showcasing notable variations in exon-intron patterns among different subfamilies. Two microRNAs, miR165/166, were found to specifically target HD-ZIP III genes with highly conserved binding sites. Most cis-acting elements identified in the promoter regions of Acoraceae HD-ZIPs are involved in modulating light and phytohormone responsiveness. Furthermore, our study revealed an independent duplication event in Ac. calamus and a one-to-multiple correspondence between HD-ZIP genes of Ac. calamus and Ac. gramineus. Expression profiles obtained from qRT-PCR demonstrated that HD-ZIP I genes are strongly induced by salinity stress, while HD-ZIP II members have contrasting stress responses in two species. HD-ZIP III and IV genes show greater sensitivity in stress-bearing roots. Taken together, these findings contribute valuable insights into the roles of HD-ZIP genes in stress adaptation and plant resilience in basal monocots, illuminating their multifaceted roles in plant growth, development, and response to abiotic stress.

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Section: The Evolutionary Dynamics Of Hd-zip Gene Familysupporting

confidence: 90%

Genome-wide characterization and expression profiling of the HD-ZIP gene family in Acoraceae under salinity and cold stress

Zhang,

Zhao,

Huang

et al. 2024

Front. Plant Sci.

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“…Peach is cultivated worldwide, due to the high nutrition and economic value. However, most of peach cultivars are susceptible to aphids, especially GPA [ 27 ]. Besides, the NLR genes in the peach genome have not been systematically analyzed and classified.…”

Section: Discussionmentioning

confidence: 99%

“…Peach is the fourth largest deciduous fruit crop in the world and has valuable nutrition [ 27 ]. Green Peach Aphid ( Myzus persicae , GPA) is the most harmful pest during peach production.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of nucleotide-binding domain leucine-rich repeat (NLR) genes and their association with green peach aphid (Myzus persicae) resistance in peach

Yu,

Wu,

Liang

et al. 2023

BMC Plant Biol

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Resistance genes (R genes) are a class of genes that are immune to a wide range of diseases and pests. In planta, NLR genes are essential components of the innate immune system. Currently, genes belonging to NLR family have been found in a number of plant species, but little is known in peach. Here, 286 NLR genes were identified on peach genome by using their homologous genes in Arabidopsis thaliana as queries. These 286 NLR genes contained at least one NBS domain and LRR domain. Phylogenetic and N-terminal domain analysis showed that these NLRs could be separated into four subfamilies (I-IV) and their promoters contained many cis-elements in response to defense and phytohormones. In addition, transcriptome analysis showed that 22 NLR genes were up-regulated after infected by Green Peach Aphid (GPA), and showed different expression patterns. This study clarified the NLR gene family and their potential functions in aphid resistance process. The candidate NLR genes might be useful in illustrating the mechanism of aphid resistance in peach.

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“…These FtUGT proteins were grouped according to the classification of the AtUGTs [75][76][77][78]. The phylogenetic trees were built using the NJ method of MEGA 11.0 via Geneious R11, with the following parameters: Jukes-Cantor model, global alignment with free end gaps, and a bootstrap value of 1000.…”

Section: Phylogenetic Analysis and Classification Of The Ftugt Gene F...mentioning

confidence: 99%

Genome-wide investigation of UDP-Glycosyltransferase family in Tartary buckwheat (Fagopyrum tataricum)

Yang,

Zhang,

Zhang

et al. 2024

BMC Plant Biol

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Background Tartary buckwheat (Fagopyrum tataricum) belongs to Polygonaceae family and has attracted increasing attention owing to its high nutritional value. UDP-glycosyltransferases (UGTs) glycosylate a variety of plant secondary metabolites to control many metabolic processes during plant growth and development. However, there have been no systematic reports of UGT superfamily in F. tataricum. Results We identified 173 FtUGTs in F. tataricum based on their conserved UDPGT domain. Phylogenetic analysis of FtUGTs with 73 Arabidopsis UGTs clustered them into 21 families. FtUGTs from the same family usually had similar gene structure and motif compositions. Most of FtUGTs did not contain introns or had only one intron. Tandem repeats contributed more to FtUGTs amplification than segmental duplications. Expression analysis indicates that FtUGTs are widely expressed in various tissues and likely play important roles in plant growth and development. The gene expression analysis response to different abiotic stresses showed that some FtUGTs were involved in response to drought and cadmium stress. Our study provides useful information on the UGTs in F. tataricum, and will facilitate their further study to better understand their function. Conclusions Our results provide a theoretical basis for further exploration of the functional characteristics of FtUGTs and for understanding the growth, development, and metabolic model in F. tataricum.

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Genome-wide identification, bioinformatics and expression analysis of HD-Zip gene family in peach

Cited by 12 publications

References 51 publications

Genome-wide characterization and expression profiling of the HD-ZIP gene family in Acoraceae under salinity and cold stress

Genome-wide characterization and expression profiling of the HD-ZIP gene family in Acoraceae under salinity and cold stress

Genome-wide identification of nucleotide-binding domain leucine-rich repeat (NLR) genes and their association with green peach aphid (Myzus persicae) resistance in peach

Genome-wide investigation of UDP-Glycosyltransferase family in Tartary buckwheat (Fagopyrum tataricum)

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